adams.flow.transformer
Class ImageJTransformer

java.lang.Object
  adams.core.ConsoleObject
      adams.core.option.AbstractOptionHandler
          adams.flow.core.AbstractActor
              adams.flow.transformer.AbstractTransformer
                  adams.flow.transformer.ImageJTransformer

All Implemented Interfaces:

AdditionalInformationHandler, CleanUpHandler, Debuggable, DebugOutputHandler, Destroyable, OptionHandler, QuickInfoSupporter, ShallowCopySupporter<AbstractActor>, SizeOfHandler, Stoppable, VariableChangeListener, Actor, ErrorHandler, InputConsumer, OutputProducer, ProvenanceSupporter, Serializable, Comparable

public class ImageJTransformer
extends AbstractTransformer
implements ProvenanceSupporter

Applies an ImageJ transformation to the incoming image and outputs the generated image(s).

Input/output:
- accepts:
adams.data.imagej.ImagePlusContainer
- generates:
adams.data.imagej.ImagePlusContainer

Valid options are:

-D <int> (property: debugLevel)
    The greater the number the more additional info the scheme may output to 
    the console (0 = off).
    default: 0
    minimum: 0
 

-name <java.lang.String> (property: name)
    The name of the actor.
    default: ImageJTransformer
 

-annotation <adams.core.base.BaseText> (property: annotations)
    The annotations to attach to this actor.
    default: 
 

-skip (property: skip)
    If set to true, transformation is skipped and the input token is just forwarded 
    as it is.
 

-stop-flow-on-error (property: stopFlowOnError)
    If set to true, the flow gets stopped in case this actor encounters an error;
     useful for critical actors.
 

-transformer <adams.data.imagej.transformer.AbstractImageJTransformer> (property: transformAlgorithm)
    The transformer to use for transformering the image.
    default: adams.data.imagej.transformer.PassThrough
 

Version:

$Revision: 6067 $

Author:

fracpete (fracpete at waikato dot ac dot nz)

See Also:

Serialized Form

Field Summary

static String	BACKUP_CURRENTIMAGES the key for storing the current images in the backup.
protected Vector<ImagePlusContainer>	m_CurrentImages the generated images.
protected AbstractImageJTransformer	m_TransformAlgorithm the transformer to apply to the image.

Fields inherited from class adams.flow.transformer.AbstractTransformer

BACKUP_INPUT, BACKUP_OUTPUT, m_InputToken, m_OutputToken

Fields inherited from class adams.flow.core.AbstractActor

m_Annotations, m_BackupState, m_DetectedObjectVariables, m_DetectedVariables, m_ErrorHandler, m_Executed, m_Executing, m_FullName, m_Headless, m_Name, m_Parent, m_Root, m_Self, m_Skip, m_StopFlowOnError, m_StopMessage, m_Stopped, m_StorageHandler, m_VariablesUpdated

Fields inherited from class adams.core.option.AbstractOptionHandler

m_DebugLevel, m_OptionManager

Fields inherited from interface adams.flow.core.Actor

FILE_EXTENSION, FILE_EXTENSION_GZ

Constructor Summary

ImageJTransformer()

Method Summary

Class[]	accepts() Returns the class that the consumer accepts.
protected Hashtable<String,Object>	backupState() Backs up the current state of the actor before update the variables.
void	defineOptions() Adds options to the internal list of options.
protected String	doExecute() Executes the flow item.
Class[]	generates() Returns the class of objects that it generates.
String	getQuickInfo() Returns a quick info about the actor, which will be displayed in the GUI.
AbstractImageJTransformer	getTransformAlgorithm() Returns the transformer in use.
String	globalInfo() Returns a string describing the object.
boolean	hasPendingOutput() Checks whether there is pending output to be collected after executing the flow item.
protected void	initialize() Initializes the members.
Token	output() Returns the generated token.
protected void	pruneBackup() Removes entries from the backup.
protected void	restoreState(Hashtable<String,Object> state) Restores the state of the actor before the variables got updated.
void	setTransformAlgorithm(AbstractImageJTransformer value) Sets the transformer to use.
String	setUp() Initializes the item for flow execution.
String	transformAlgorithmTipText() Returns the tip text for this property.
void	updateProvenance(ProvenanceContainer cont) Updates the provenance information in the provided container.
void	wrapUp() Cleans up after the execution has finished.

Methods inherited from class adams.flow.transformer.AbstractTransformer

execute, input, postExecute, reset

Methods inherited from class adams.flow.core.AbstractActor

annotationsTipText, canInspectOptions, canPerformSetUpCheck, cleanUp, compareTo, debug, destroy, equals, findVariables, findVariables, findVariables, forceVariables, forCommandLine, forName, getAdditionalInformation, getAnnotations, getDefaultName, getDetectedVariables, getErrorHandler, getFlowActors, getFullName, getName, getNextSibling, getParent, getPreviousSibling, getRoot, getSkip, getStopFlowOnError, getStopMessage, getStorageHandler, getVariables, handleError, handleException, hasErrorHandler, hasStopMessage, index, isBackedUp, isExecuted, isExecuting, isFinished, isHeadless, isStopped, nameTipText, performSetUpChecks, preExecute, pruneBackup, setAnnotations, setErrorHandler, setHeadless, setName, setParent, setSkip, setStopFlowOnError, setVariables, shallowCopy, shallowCopy, sizeOf, skipTipText, stopExecution, stopExecution, stopFlowOnErrorTipText, updateDetectedVariables, updatePrefix, updateVariables, variableChanged

Methods inherited from class adams.core.option.AbstractOptionHandler

cleanUpOptions, debug, debugLevelTipText, finishInit, getDebugLevel, getOptionManager, isDebugOn, newOptionManager, setDebugLevel, toCommandLine, toString

Methods inherited from class adams.core.ConsoleObject

getDebugging, getSystemErr, getSystemOut

Methods inherited from class java.lang.Object

clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface adams.flow.core.Actor

cleanUp, compareTo, debug, destroy, equals, findVariables, getAnnotations, getDefaultName, getDetectedVariables, getErrorHandler, getFullName, getName, getNextSibling, getParent, getPreviousSibling, getRoot, getSkip, getStopFlowOnError, getStopMessage, getStorageHandler, getVariables, handleError, hasErrorHandler, hasStopMessage, index, isExecuted, isFinished, isHeadless, isStopped, setAnnotations, setErrorHandler, setHeadless, setName, setParent, setSkip, setStopFlowOnError, setVariables, sizeOf, stopExecution, stopExecution, variableChanged

Methods inherited from interface adams.core.AdditionalInformationHandler

getAdditionalInformation

Methods inherited from interface adams.core.option.OptionHandler

cleanUpOptions, getOptionManager

Field Detail

BACKUP_CURRENTIMAGES

public static final String BACKUP_CURRENTIMAGES

the key for storing the current images in the backup.

See Also:

Constant Field Values

m_TransformAlgorithm

protected AbstractImageJTransformer m_TransformAlgorithm

the transformer to apply to the image.

m_CurrentImages

protected Vector<ImagePlusContainer> m_CurrentImages

the generated images.

Constructor Detail

ImageJTransformer

public ImageJTransformer()

Method Detail

globalInfo

public String globalInfo()

Returns a string describing the object.

Specified by:

globalInfo in class AbstractOptionHandler

Returns:

a description suitable for displaying in the gui

defineOptions

public void defineOptions()

Adds options to the internal list of options.

Specified by:

defineOptions in interface OptionHandler

Overrides:

defineOptions in class AbstractActor

initialize

protected void initialize()

Initializes the members.

Overrides:

initialize in class AbstractActor

setTransformAlgorithm

public void setTransformAlgorithm(AbstractImageJTransformer value)

Sets the transformer to use.

Parameters:

value - the transformer

getTransformAlgorithm

public AbstractImageJTransformer getTransformAlgorithm()

Returns the transformer in use.

Returns:

the transformer

transformAlgorithmTipText

public String transformAlgorithmTipText()

Returns the tip text for this property.

Returns:

tip text for this property suitable for displaying in the GUI or for listing the options.

getQuickInfo

public String getQuickInfo()

Returns a quick info about the actor, which will be displayed in the GUI.

Specified by:

getQuickInfo in interface QuickInfoSupporter

Specified by:

getQuickInfo in interface Actor

Overrides:

getQuickInfo in class AbstractActor

Returns:

null if no info available, otherwise short string

accepts

public Class[] accepts()

Returns the class that the consumer accepts.

Specified by:

accepts in interface InputConsumer

Returns:

the Class of objects that can be processed

generates

public Class[] generates()

Returns the class of objects that it generates.

Specified by:

generates in interface OutputProducer

Returns:

adams.data.imagej.ImagePlusContainer.class

pruneBackup

protected void pruneBackup()

Removes entries from the backup.

Overrides:

pruneBackup in class AbstractActor

backupState

protected Hashtable<String,Object> backupState()

Backs up the current state of the actor before update the variables.

Overrides:

backupState in class AbstractTransformer

Returns:

the backup

restoreState

protected void restoreState(Hashtable<String,Object> state)

Restores the state of the actor before the variables got updated.

Overrides:

restoreState in class AbstractTransformer

Parameters:

state - the backup of the state to restore from

setUp

public String setUp()

Initializes the item for flow execution.

Specified by:

setUp in interface Actor

Overrides:

setUp in class AbstractActor

Returns:

null if everything is fine, otherwise error message

doExecute

protected String doExecute()

Executes the flow item.

Specified by:

doExecute in class AbstractActor

Returns:

null if everything is fine, otherwise error message

hasPendingOutput

public boolean hasPendingOutput()

Checks whether there is pending output to be collected after executing the flow item.

Specified by:

hasPendingOutput in interface OutputProducer

Overrides:

hasPendingOutput in class AbstractTransformer

Returns:

true if there is pending output

output

public Token output()

Returns the generated token.

Specified by:

output in interface OutputProducer

Overrides:

output in class AbstractTransformer

Returns:

the generated token

wrapUp

public void wrapUp()

Cleans up after the execution has finished.

Specified by:

wrapUp in interface Actor

Overrides:

wrapUp in class AbstractTransformer

updateProvenance

public void updateProvenance(ProvenanceContainer cont)

Updates the provenance information in the provided container.

Specified by:

updateProvenance in interface ProvenanceSupporter

Parameters:

cont - the provenance container to update